Problem Corrupt BD - What can I do?

I got a very rare BD in the mail the other day. Twelve Kingdoms: A Great Distance in the Wind, the Sky at Dawn. They only made about 25,000 copies of this.

Here's the issue. When SONY revealed the first Bluray protoypes, they boasted the disc had superior error-correction; and a scratch-resistant coating. Here's a picture of the back of the disc:

Now, with a blind-eye, there isn't much to look at. The disc seems immaculate. However. It is not, or I wouldn't be writing this thread. Along the surface are what look like circular scratches. I say look like, because upon further inspection the "scratches" actually look like very small dots, grouped close together, with a large dot where the "scratch" trails off. There are about four of these "scratches."

I took the disc in to be doctored, at a store that uses a $6000 machine. The "scratches" seemed unaffected. After bringing it back home, it stopped playing at the same spots. I then used an AACS descrambler and ISOBuster to run a full recovery on the disc, at 41.2% the errors began to occur, so I choose to fill the sectors with zeroes, and applied this to the whole recovery session.

I now have a backup of the disc, but with truncated data. A friend of mine was able to help by tracking down rips of the episodes on that disc. Now what I'm thinking is, if I could, I'll take the menus & special features (which ripped just fine) and then use the rips I have, find the problem areas and remux in the video, audio & subtitle streams in those areas, and then author the backup disc with the "repaired sections."

The only way I can think of doing so, is taking the original M2TS, drop it into a video production software, cut out the problem areas and drop in the repair rips, trimming them down to the affected frames, encode the new video file with no audio, ensure that the number of frames and video length match up and then use a remux software to drop in the audio and subtitles from the rips (as the audio and subs from the original M2TS would also be truncated).

Any suggestions on a less time-consuming workaround or preferable software, like perhaps Handbrake, etc etc. Thanks in advance for any suggestions.

Thank you scropNZ for the input. But what I'm looking into doing is taking the main video and basically slipstream in clean video where the data is corrupt. I already have all the menus and everything ripped.